rs7953528

Variant names:

• chr12-27864226-T-A
• rs7953528

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.136 in 152,254 control chromosomes in the GnomAD database, including 1,733 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.14 (1733 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.323

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20670 AN: 152136 Hom.: 1732 Cov.: 32

Gnomad AFR AF: 0.0442

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.155

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.136 AC: 20666 AN: 152254 Hom.: 1733 Cov.: 32 AF XY: 0.135 AC XY: 10047 AN XY: 74442

Gnomad4 AFR AF: 0.0441

Gnomad4 AMR AF: 0.125

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.269

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.155

Alfa AF: 0.178 Hom.: 1435

Bravo AF: 0.131

Asia WGS AF: 0.177 AC: 615 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	6.8
DANN	Benign	0.87

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7953528; hg19: chr12-28017159;